All Published Workflows
70 workflows that have been reviewed and published
This Snakemake pipeline implements the GATK best-practices workflow
This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse...
JSON
raw sequence reads
Variant calling
genetic variants
delly
gatk
rust-bio-tools
snakemake-wrapper-utils
tabix
BCFtools
BEDTools
Bowtie 2
BWA
Cutadapt
FastQC
fgbio
FreeBayes
mosdepth
MultiQC
Pandas
Picard
SAMtools
Snakemake
Variant Effect Predictor (VEP)
vembrane
numpy
oschmod
sklearn
statsmodels
Varlociraptor
DNA
Snakemake-based workflow for detecting structural variants in genomic data
Structural variants (SVs) are an important class of genetic variation implicated in a wide array of genetic diseases. sv-ca...
Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)
Note: for SVDSS (v1), please refer to v1.0.5-fix and 6fa89f0 . SVDSS is a novel method for discovery of structural...
Use an ensemble of variant callers to call variants from ATAC-seq data
A pipeline for running an ensemble of variant callers to predict variants from ATAC-seq reads. The entire pipeline is made up...
Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
snpArcher is a reproducible workflow optimized for nonmodel organisms and comparisons across datasets, built on the Snakema...
Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
A reproducible and scalable workflow for transparent and robust SARS-CoV-2
variant calling and lineage assignment with com...
JSON
raw sequence reads
Variant calling
genetic variants
delly
nanofilt
rust-bio-tools
snakemake-wrapper-utils
tabix
BCFtools
Biopython
BWA
CANU
Consensus
fastp
FastQC
fgbio
FreeBayes
GFFutils
kallisto
Kraken
Krona
Medaka
metaspades
Minimap2
MultiQC
Pandas
Pangolin
Picard
Quant
QUAST
SAMtools
Snakemake
Variant Effect Predictor (VEP)
vembrane
altair
intervaltree
numpy
pysam
requests
Varlociraptor
COVID19 Risk Mitigation
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
Documentation : https://sanjaynagi.github.io/rna-seq-pop/
Walkthrough : https://www.youtube.com/watch?v=5QQe7DLHO4...
FASTQ-illumina
JSON
Sample annotation
Variant calling
genetic variants
snakemake-wrapper-utils
EnhancedVolcano
BCFtools
DESeq2
fastp
FreeBayes
GLUE
HISAT2
kallisto
mosdepth
MultiQC
Pandas
pheatmap
Quant
SAMBLASTER
SAMtools
sleuth
Snakemake
snpEff
Vcflib
data.table
dplyr
ggplot2
ggrepel
jsonlite
openxlsx
RColorBrewer
tidyverse
ipykernel
matplotlib
matplotlib-venn
numpy
papermill
pop-tools
scipy
zarr
Population genomics
A repo for the Twist HiFi capture/snakemake workflow
This is a snakemake workflow for analyzing targeted HiFi sequence datasets. The workflow was designed for Twist gene pane...
A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets
A Snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB) data (and other custom benchm...
This is an human RNAseq variant calling workflow, following the GATK pipeline. Also includes ADAR-site elimination.
Clone the git repository with the command:
git clone https://github.com/durrantmm/rnaseq_variant_calling_workflow.git This wo...
(S)train (A)ssignment from (M)etagen(O)me (S)NP (A)nalysis.
SAMOSA is a Snakemake computational workflow for performing strain level detection from Metagenomic samples. The pipeline is ...